Reference genomes

Description

The same reference genomes are used across many different projects. Although each user may prefer to have its own copy of the genome sequence, there is a genomes folder in datasets that can serve as the collective storage of reference genomes.

You can find the full path to the directory here: /workspace/datasets/genomes/

The contents of this folder are the following:

GRCh37
GRCh38
iGenomes
iGenomes_2022
purple_resources
README.txt
Saccharomyces_cerevisiae
SageGermlinePon.hg38.98x.vcf.gz
SAGE_resources

GRCh37 -> contains only the FASTA file of the genome assembly GRCh37

GRCh38 -> contains the genomic sequence of GRCh38 human genome assembly with several index files, as well as some annotation files.

iGenomes -> contains the illumina Homo sapiens genomes in different versions and from different origins (NCBI, GATK, UCSC)

iGenomes_2022 -> contains the illumina Homo sapiens genome for version GRCh38 and from NCBI

purple_resources -> contains two files seemingly related to a panel of normals.

Saccharomyces_cerevisiae -> contains information of the genome of this species and it was downloaded from UCSC iGenomes.

SageGermlinePon... and SAGE resources are resources related to running SAGE.

Recommendations

It would be good to get used to use the reference files that are here avoiding the creation of multiple copies of the same files all along the cluster.

Reference

Ferriol Calvet

2023/03/16